View source for Initiation of signal transduction

[[Category:Signaling]]
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==Current Terms==

 [Term]
 id: GO:0023036
 name: initiation of signal transduction
 namespace: biological_process
 def: "The process in which a signal causes activation of a receptor, for example, via a conformation change." [GOC:mtg_sig]
 comment: Note that this term is intended for the annotation of both ligands and receptors.
 synonym: "signal reception" RELATED []
 is_a: GO:0009987 ! cellular process
 relationship: part_of GO:0007165 ! signal transduction
 creation_date: 2010-02-16T09:30:50Z

 initiation of signal transduction ; GO:0023036
 signal initiation by diffusible mediator ; GO:0023038
 initiation of adrenergic receptor signal transduction ; GO:0071876
 signal initiation by amino acid ; GO:0023006
 signal initiation by chemical mediator ; GO:0023047
 signal initiation by lipid mediator ; GO:0023048
 signal initiation by neurotransmitter ; GO:0023005
 activation of dopamine receptor signaling pathway ; GO:0023004
 signal initiation by protein/peptide mediator ; GO:0023049
 initiation of Roundabout signal transduction ; GO:0035555
 initiation of T cell receptor signaling ; GO:0023009
 initiation of T cell receptor signaling by binding of a MHC complex to T cell receptor ; GO:0023012
 ligand binding to T cell receptor ; GO:0023007
 positive regulation of initiation of T cell receptor signaling ; GO:0023011
 regulation of initiation of T cell receptor signaling ; GO:0023010
 signal initiation by peptide hormone ; GO:0023055
 signal initiation by light ; GO:0023037
 signal initiation by mechanical effect ; GO:0023053
 signal initiation by physical damage ; GO:0023039
 signal initiation by stretch effect ; GO:0023054

==Problems with the current term==

* The comment states that the term can be used to annotate both ligands and receptors, however many of the children terms (E.g. initiation of signal transduction by mechanical effect) cover cases where the ligand is not a gene product.

* The definition is more geared to annotation of ligands rather than receptors.

* The definition does not state where initiation of signal transduction ends. At the February 2011 signaling workshop, we asked whether initiation of signal transduction ends with an activated receptor, or when an activated receptor has passed the signal to the next signaling molecule, and it wasn't possible to reach a standard for all pathways.

* With the addition of links between the function terms: 'receptor activity ; GO:0004872' and 'receptor agonist activity ; GO:0048018' and the process term 'signal transduction ; GO:0007165' a grouping term in process is not particularly useful.

==Proposal Overview==

* OBSOLETE 'initiation of signal transduction ; GO:0023036 and it's children.
* REPLACE the existing annotations with 'receptor activity' and 'receptor antagonist activity' terms, along with 'signal transduction terms'.

==Proposal Specifics==

 <font color="purple">initiation of signal transduction ; GO:0023036</font color>
 consider: receptor activity ; GO:0004872
 consider: receptor agonist activity ; GO:0004872
 consider: signal transduction ; GO:0007165

 <font color="purple">signal initiation by diffusible mediator</font color>
 consider: paracrine signaling ; GO:0038001
 consider: signal transduction ; GO:0007165
 consider: receptor activity ; GO:0004872
 consider: receptor agonist activity ; GO:0048018

 <font color="purple">initiation of adrenergic receptor signal transduction ; GO:0071876</font color>
 consider: adrenergic receptor activity ; GO:0004935
 consider: adrenergic receptor signaling pathway ; GO:0071875
 consider: signal transduction ; GO:0007165
 consider: cellular response to epinephrine stimulus ; GO:0071872
 consider: cellular response to norepinephrine stimulus ; GO:0071874
 consider: hormone activity ; GO:0005179

 <font color="purple">signal initiation by amino acid ; GO:0023006</font color>
 consider: glutamate receptor activity ; GO:0008066
 consider: glutamate signaling pathway ; GO:0007215
 consider: cellular response to amino acid stimulus ; GO:0071230

 <font color="purple">signal initiation by chemical mediator ; GO:0023047</font color>
 consider: signal transduction ; GO:0007165
 consider: receptor activity ; GO:0004872
 consider: cellular response to chemical stimulus ; GO:0070887

 <font color="purple">signal initiation by lipid mediator ; GO:0023048</font color>
 consider: signal transduction ; GO:0007165
 consider: bioactive lipid receptor activity ; GO:0045125

 <font color="purple">signal initiation by neurotransmitter ; GO:0023005</font color>
 consider: signal transduction ; GO:0007165
 consider: neurotransmitter receptor activity ; GO:0030594

 <font color="purple">signal initiation by light ; GO:0023037</font color>
 consider: photoreceptor activity ; GO:0009881
 consider: signal transduction ; GO:0007165
 consider: blue light signaling pathway ; GO:0009785
 consider: far-red light signaling pathway ; GO:0010018
 consider: red or far-red light signaling pathway ; GO:0010017
 consider: red light signaling pathway ; GO:0010161

 <font color="purple">activation of dopamine receptor signaling pathway ; GO:0023004</font color>
 consider: signal transduction ; GO:0007165
 consider: dopamine receptor signaling pathway ; GO:0007212
 NB: Note that ligands are part of the signaling pathway.

 <font color="purple">signal initiation by protein/peptide mediator ; GO:0023049</font color>
 consider: signal transduction ; GO:0007165
 consider: receptor activity ; GO:0004872
 consider: receptor agonist activity ; GO:0048018

 <font color="purple">initiation of Roundabout signal transduction ; GO:0035555</font color>
 consider: signal transduction ; GO:0007165
 consider: Roundabout signaling pathway ; GO:0035385
 consider: Roundabout binding ; GO:0048495
 NB: Note that ligands (SLIT in this case) are part of the signaling pathway.

 <font color="purple">initiation of T cell receptor signaling ; GO:0023009</font color>
 consider: T cell receptor signaling pathway ; GO:0050852
 consider: T cell receptor complex ; GO:0042101

 <font color="purple">initiation of T cell receptor signaling by binding of a MHC complex to T cell receptor ; GO:0023012</font color>
 consider: T cell receptor signaling pathway ; GO:0050852
 consider: T cell receptor complex ; GO:0042101

 <font color="purple">regulation of initiation of T cell receptor signaling ; GO:0023010</font color>
 consider: regulation of T cell receptor signaling pathway ; GO:0050856 

 <font color="purple">positive regulation of initiation of T cell receptor signaling ; GO:0023011</font color>
 consider: positive regulation of T cell receptor signaling pathway ; GO:0050862

 <font color="purple">ligand binding to T cell receptor ; GO:0023007</font color>
 consider: T cell receptor binding ; GO:0042608
 consider: T cell receptor complex ; GO:0042101

 <font color="purple">signal initiation by peptide hormone ; GO:0023055</font color>
 consider: hormone-mediated signaling pathway ; GO:0009755
 consider: ligand-dependent nuclear receptor activity ; GO:0004879
 consider: hormone activity ; GO:0005179

 <font color="purple">signal initiation by mechanical effect ; GO:0023053</font color>
 consider: signal transduction ; GO:0007165
 consider: cellular response to mechanical stimulus ; GO:0071260

 <font color="purple">signal initiation by physical damage ; GO:0023039</font color>
 consider: signal transduction ; GO:0007165
 consider: cellular response to stress ; GO:0033554

 <font color="purple">signal initiation by stretch effect ; GO:0023054</font color>
 consider: signal transduction ; GO:0007165

==Existing annotations==

The low number of annotations to these terms agrees with the concern that the terms are confusing and poorly defined. Annotations are as follows:

 initiation of signal transduction ; GO:0023036	                    (0 direct annotations)
 signal initiation by diffusible mediator ; GO:0023038	            (0 direct annotations)
 initiation of adrenergic receptor signal transduction ; GO:0071876 (0 direct annotations)
 signal initiation by amino acid ; GO:0023006	                    (20 ISS and IMP annotations from UniProt for glutamate receptors)
 signal initiation by chemical mediator ; GO:0023047	            (0 direct annotations)
 signal initiation by lipid mediator ; GO:0023048                   (1 BHF-UCL)
 signal initiation by neurotransmitter ; GO:0023005                 (4 annotations: 1 EA Ensembl, 3 manual BHF-UCL to purinoreceptors)
 activation of dopamine receptor signaling pathway ; GO:0023004	    (0 direct annotations)
 signal initiation by protein/peptide mediator ; GO:0023049	    (0 direct annotations)
 initiation of Roundabout signal transduction ; GO:0035555	    (1 annotation: BHF-UCL to SLIT2)
 initiation of T cell receptor signaling ; GO:0023009	            (0 direct annotations)
 initiation of T cell receptor signaling by binding of a MHC complex to T cell receptor ; GO:0023012	(0 direct annotations)
 ligand binding to T cell receptor ; GO:0023007	                    (0 direct annotations)
 positive regulation of initiation of T cell receptor signaling ; GO:0023011	(1 annotation: BHF-UCL)
 regulation of initiation of T cell receptor signaling ; GO:0023010	        (0 direct annotations)
 signal initiation by peptide hormone ; GO:0023055	                        (0 direct annotations)
 signal initiation by light ; GO:0023037	                                (0 direct annotations)
 signal initiation by mechanical effect ; GO:0023053	                        (0 direct annotations)
 signal initiation by physical damage ; GO:0023039	                        (0 direct annotations)
 signal initiation by stretch effect ; GO:0023054	                        (0 direct annotations)




==OUTCOME==

Initiation of signal transduction terms were obsoleted from GO in May 2011 (version 1.1957).